Synthetic PhiX174 viruses created by Autodesk

Autodesk

Synthetic PhiX174 viruses created by Autodesk

Science


Autodesk, which develops design software for building very big things, just built a very small thing.

Its own virus.

The San Rafael, Calif., company has revealed to Re/code that last month it produced a synthetic Phi-X174 bacteriophage, a virus that infects the E. coli bacteria but is totally benign for humans. They conducted the experiment in a controlled lab setting with the help of Dr. Paul Jaschke of Stanford University.

The effort was a sort of scientific homage to the work of the J. Craig Venter Institute, which first produced the self-replicating synthetic virus back in 2003, following a more than five-year research effort. In Autodesk’s case, it took a little more than two weeks and about $1,000.

That achievement says a lot about how far the science of synthetic biology has come — and a lot about where Autodesk is going.

Andrew Hessel, distinguished researcher at Autodesk.

Courtesy: Autodesk Andrew Hessel, a distinguished researcher at Autodesk.

“These viruses started their existence as a file on my laptop and a [purchase order] number with a DNA synthesis vendor!” said Andrew Hessel, a distinguished researcher with Autodesk’s new Bio/Nano Programmable Matter group, in an email.

“It’s a 3-D printed virus,” he added. “With further development of the process, the designs, the design software — we can help scientists make useful applications, like personalized cancer treatments or new vaccines.”

Autodesk, which is still best known for producing AutoCAD software for architects and engineers, wants to stake a claim in the center of a promising new world.

The company is collaborating with leading scientists on a research effort known as “Project Cyborg.” They’re attempting to build a software platform that could enable greater design complexity as researchers work to engineer self-assembling DNA, proteins, viruses, cells, tissues and more.

The company first revealed its ambitions at TED in 2013 and has been refining its approach since. Hessel told Re/code the company is gearing up for the next phase of product development, putting the tools into the hands of a broader group of researchers.

“There’s never been a comprehensive set of tools in this space,” Hessel said in an interview. “So we’re looking at whether we can build accessible software based on what we’ve learned in order to facilitate laboratory work, bioengineering and nano design.”

In the Ted Talk below, MIT’s Skylar Tibbits discusses how using Project Cyborg assists the design process for what he calls 4-D printing, where the fourth dimension is time — as physical products self assemble after they’re produced:

A key goal of Project Nano is to connect existing software tools in the field, so that they can talk to each other as well as with Autodesk applications like Maya, an animation tool used in Hollywood blockbusters.

Various research labs have attacked parts of this problem. The Baker Laboratory at the University of Washington created Rosetta, widely used software for designing proteins, as Re/code wrote about last month.

Shawn Douglas, an assistant professor at UC San Francisco, developed Cadnano for DNA design and collaborated with Project Cyborg to improve the 3-D functionality of the open source tool.

Meanwhile, private DNA synthesis shop Gen9 is working on its own software specifically to support “visualization and design for manufacturability,” Chief Executive Kevin Munnelly said.

At this stage, it’s unclear which parties will end up as partners, rivals or something else in the emerging space, he added.

“It’s still a very early industry, so [it could be] cooperation or cooper-etition, data sharing or API linking, all of those things can happen,” he said.

Of course, putting these tools into more people’s hands carries risks as well. While scientists see great potential to create novel medicines, vaccines and nanomaterials, bad actors could attempt to use them to create bio-weapons.

Hessel himself has pointed this out, notably by co-writing a memorable piece for the Atlantic titled “Hacking the President’s DNA.”

DNA synthesis companies like Gen9 have already put some safeguards in place, including automatic pre-screening of DNA orders for whole or partial sequences that carry telltale signs of pathogens.

Autodesk didn’t have any explicit commercial purpose in creating the viruses, which the company has already destroyed. It mainly wanted to walk through the process, including ordering precisely specified DNA strands from synthesis shops, to gain a better sense of where the market stands.

“I thought opening up this channel and understanding it was very important,” Hessel said. “The take-home message for me is that genome synthesis today has significantly improved over the years and now is capable of routinely producing about 5,000 base pairs without much trouble.”

The Phi-X174 virus genome consists of 5,386 base pairs of nucleotides, the basic structural unit of DNA. By way of comparison, the human genome stretches out to 3 billion.

Commercializing anything out of Project Cyborg could still be years away. So it remains to be seen whether Autodesk is timing the market right — or will ultimately emerge as a leader in the space.

But it’s increasingly clear there’s a giant opportunity in the nano world.

“They see synthetic biology and bionanotechnology as a future industry,” Douglas said. “The way you get a foothold and become relevant is by experimenting; try out different things and that knowledge accumulates over time.”

To learn more about synthetic biology, check out the primer in the video below — or the many additional resources on Andrew Hessel’s site.



0 comments
Follow

Get every new post delivered to your Inbox.

Join 301,163 other followers